There were standing orders to shoot civilians on sight. Ask pretty much any marine who served in Iraq whether they were ordered to fire only at armed individuals, or if their orders were to assume that any male over a certain age, who just happened to be in the contested area was an insurgent, and to shoot to kill.
I’ve got a good friend who followed these orders and is so haunted by them (rightfully so) that he’s on a cocktail of psych meds and has attempted to off himself a couple of times. In his particular case, it turns out that not every ~13 year old male happens to be an armed insurgent…
This is not in any way meant to diminish your point that war crimes did not happen earlier, in fact, beyond Tokyo, crimes in Vietnam are pretty well documented.